changed reading of name file to use buffered reads. note the splitAtWhiteSpace functi...

[mothur.git] / classifyseqscommand.cpp

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index b6dc24fe5751867c6b79f71fb50e3b7b74ad75a6..158069e7ae596e3eebd6a9d2da5834ec3529dcdc 100644 (file)
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -919,8 +919,8 @@ int ClassifySeqsCommand::createProcesses(string taxFileName, string tempTaxFile,
                else { m->mothurRemove(accnos); } //remove so other files can be renamed to it
         
                for(int i=0;i<processIDS.size();i++){
-                       appendTaxFiles((taxFileName + toString(processIDS[i]) + ".temp"), taxFileName);
-                       appendTaxFiles((tempTaxFile + toString(processIDS[i]) + ".temp"), tempTaxFile);
+                       m->appendFiles((taxFileName + toString(processIDS[i]) + ".temp"), taxFileName);
+                       m->appendFiles((tempTaxFile + toString(processIDS[i]) + ".temp"), tempTaxFile);
             if (!(m->isBlank(accnos + toString(processIDS[i]) + ".temp"))) {
                                nonBlankAccnosFiles.push_back(accnos + toString(processIDS[i]) + ".temp");
                        }else { m->mothurRemove((accnos + toString(processIDS[i]) + ".temp"));  }
@@ -934,7 +934,7 @@ int ClassifySeqsCommand::createProcesses(string taxFileName, string tempTaxFile,
                        rename(nonBlankAccnosFiles[0].c_str(), accnos.c_str());
                        
                        for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
-                               appendTaxFiles(nonBlankAccnosFiles[h], accnos);
+                               m->appendFiles(nonBlankAccnosFiles[h], accnos);
                                m->mothurRemove(nonBlankAccnosFiles[h]);
                        }
                }else { //recreate the accnosfile if needed
@@ -951,30 +951,6 @@ int ClassifySeqsCommand::createProcesses(string taxFileName, string tempTaxFile,
                exit(1);
        }
 }
-/**************************************************************************************************/
-
-void ClassifySeqsCommand::appendTaxFiles(string temp, string filename) {
-       try{
-               
-               ofstream output;
-               ifstream input;
-               m->openOutputFileAppend(filename, output);
-               m->openInputFile(temp, input);
-               
-               while(char c = input.get()){
-                       if(input.eof())         {       break;                  }
-                       else                            {       output << c;    }
-               }
-               
-               input.close();
-               output.close();
-       }
-       catch(exception& e) {
-               m->errorOut(e, "ClassifySeqsCommand", "appendTaxFiles");
-               exit(1);
-       }
-}
-
 //**********************************************************************************************************************
 
 int ClassifySeqsCommand::driver(linePair* filePos, string taxFName, string tempTFName, string accnos, string filename){